Linear Dichroism Data Research Articles

Enhanced Magnetic Anisotropy and Orbital Symmetry Breaking in Manganite Heterostructures

AbstractManipulating magnetic anisotropy in complex oxide heterostructures has attracted much attention. Here, three interface‐engineering approaches are applied to address two general issues with controlling magnetic anisotropy in the La2/3Sr1/3MnO3 heterostructure. One is the paradox arising from the competition between Mn3d–O2p orbital hybridization and MnO6 crystal field. The other is the interfacial region where the nonuniform MnO bond length d and MnOMn bond angle θ disturb the structural modulation. When the interfacial region is suppressed in the interface‐engineered samples, the lateral magnetic anisotropy energy is increased eighteen times. The d‐mediated anisotropic crystal filed that overwhelms the orbital hybridization causes the lateral symmetry breaking of the Mn 3dx2−y2 orbital, resulting in enhanced magnetic anisotropy. This is different from the classic Jahn–Teller effect where the lateral symmetry is always preserved. Moreover, the quantitative analysis on X‐ray linear dichroism data suggests a direct correlation between Mn 3dx2−y2 orbital symmetry breaking and magnetic anisotropy energy. The findings not only advance the understanding of magnetic anisotropy in manganite heterostructures but also can be extended to other complex oxides and perovskite materials with correlated degrees of freedom.

Large effect of metal substrate on magnetic anisotropy of Co on hexagonal boron nitride

We combine x-ray absorption spectroscopy (XAS), x-ray magnetic circular dichroism (XMCD) and x-ray magnetic linear dichroism (XMLD) data with first principles density functional theory (DFT) calculations and a multiorbital many-body Hamiltonian approach to understand the electronic and magnetic properties of Co atoms adsorbed on h-BN/Ru(0001) and h-BN/Ir(111). The XAS line shape reveals, for both substrates, an electronic configuration close to 3d8, corresponding to a spin S = 1. Magnetic field dependent XMCD data show large (14 meV) out-of-plane anisotropy on h-BN/Ru(0001), while it is almost isotropic (tens of μeV) on h-BN/Ir(111). XMLD data together with both DFT calculations and the results of the multiorbital Hubbard model suggest that the dissimilar magnetic anisotropy originates from different Co adsorption sites, namely atop N on h-BN/Ru(0001) and 6-fold hollow on h-BN/Ir(111).

Chemical Aspects of the Candidate Antiferromagnetic Topological Insulator MnBi2Te4

Crystal growth of MnBi$_{2}$Te$_{4}$ has delivered the first experimental corroboration of the 3D antiferromagnetic topological insulator state. Our present results confirm that the synthesis of MnBi$_{2}$Te$_{4}$ can be scaled-up and strengthen it as a promising experimental platform for studies of a crossover between magnetic ordering and non-trivial topology. High-quality single crystals of MnBi$_{2}$Te$_{4}$ are grown by slow cooling within a narrow range between the melting points of Bi$_{2}$Te$_{3}$ (586 {\deg}C) and MnBi$_{2}$Te$_{4}$ (600 {\deg}C). Single crystal X-ray diffraction and electron microscopy reveal ubiquitous antisite defects in both cation sites and, possibly, Mn vacancies. Powders of MnBi$_{2}$Te$_{4}$ can be obtained at subsolidus temperatures, and a complementary thermochemical study establishes a limited high-temperature range of phase stability. Nevertheless, quenched powders are stable at room temperature and exhibit long-range antiferromagnetic ordering below 24 K. The expected Mn(II) out-of-plane magnetic state is confirmed by the magnetization, X-ray photoemission, X-ray absorption and linear dichroism data. MnBi$_{2}$Te$_{4}$ exhibits a metallic type of resistivity in the range 4.5-300 K. The compound is an n-type conductor that reaches a thermoelectric figure of merit up to ZT = 0.17. Angle-resolved photoemission experiments provide evidence for a surface state forming a gapped Dirac cone.

Comparison of the Binding Geometry of Free-Base and Hexacoordinated Cationic Porphyrins to A- and B-Form DNA.

Although the transition from B-DNA to the A-form is essential for many biological concerns, the properties of this transition have not been resolved. The B to A equilibrium can be analyzed conveniently because of the significant changes in circular dichroism (CD) and absorption spectrum. CD and linear dichroism (LD) methods were used to examine the binding of water-soluble meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) and its derivatives, Co-TMPyP, with B- and A-calf thymus DNA. B- to A-transitions occurred when the physiological buffer was replaced with a water-ethanol mixture (∼80 v/v %), and the fluorescence emission spectra of TMPyP bound to DNA showed a different pattern under ethanol–water conditions and water alone. The featureless broad emission bands of TMPyP were split into two peaks near at 658 and 715 nm in the presence of DNA under an aqueous solution. In the case of an ethanol–water system, however, the emission bands are split in two peaks near at 648 and 708 nm and 656 and 715 nm with and without DNA, respectively. This may be due to a change in the solution polarity. On the basis of the CD and LD data, TMPyP interacts with B-DNA via intercalation at a low ratio under a low ionic strength, 1 mM sodium phosphate. On the other hand, the interaction with A-DNA (80 v/v % ethanol–water system) occurs in a nonintercalating manner. This difference might be because the structural conformations, such as the groove of A-DNA, are not as deep as in B-DNA and the bases are much more tilted. In the case of Co-TMPyP, porphyrin binds preferably via an outside self-stacking mode with B- and A-DNA.

Optimized interferometric setup for chiral and achiral ultrafast IR spectroscopy.

We report an actively stabilized interferometer-based set-up for the detection of vibrational circular dichroism (VCD) and optical rotatory dispersion (VORD) with femtosecond laser pulses. Our approach combines and improves elements of several previous measurement strategies, including signal amplification in a crossed polarizer configuration, precise control and modulation of polarization, phase stability, tight focusing, broad-band detection and spectral interferometry. Their importance for static and transient measurements is motivated by a signal analysis based on Jones matrices and response theory. Only depending on the pump-beam polarization, the set-up can selectively detect transient VCD and VORD or transient linear birefringence (LB) and linear dichroism (LD), which usually constitute the dominant artifacts in the chiral measurements. For illustration we present transient LB and LD data of an achiral Rhenium carbonyl complex, detected simultaneously by spectral interferometry, and we analyze residual background signals in the experimental configuration for transient chiral spectroscopy.

Oxidized polyethylene films for orienting polar molecules for linear dichroism spectroscopy

Stretched polyethylene (PE) films have been used to orient small molecules for decades by depositing solutions on their surface and allowing the solvent to evaporate leaving the analyte absorbed on the polymer film. However, the non-polar hydrophobic nature of PE is an obstacle to aligning polar molecules and biological samples. In this work PE film was treated with oxygen plasma in order to increase surface hydrophilicity. Different treatment conditions were evaluated using contact angle measurement and X-ray photoelectron spectroscopy. Treated PE (PE(OX)) films are shown to be able to align molecules of different polarities including progesterone, 1-pyrenecarboxaldehyde, 4',6-diamidino-2-phenylindole (DAPI) and anthracene. The degree of alignment of each molecule was studied by running series of linear dichroism (LD) experiments and the polarizations of electronic transition moments were determined. For the first time optimal conditions (such as stretching factor and concentration of the sample) for stretched film LD were determined. PE(OX) aligning ability was compared to that of normal PE films. Progesterone showed a slightly better alignment on PE(OX) than PE. 1-Pyrenecarboxaldehyde oriented differently on the two different films which enabled transition moment assignment for this low symmetry molecule. DAPI (which does not align on PE) aligned well on PE(OX) and enabled us to obtain better LD data than had previously been collected with polyvinyl alcohol. Anthracene alignment and formation of dimers and higher order structures were studied in much more detail than previously possible, showing a variety of assemblies on PE and PE(OX) films.

Probing the structure of long DNA molecules in solution using synchrotron radiation linear dichroism

Linear dichroism (LD), a spectroscopic method for aligned samples, has been used with a synchrotron radiation source to reveal insights into the structure and stability of DNA with increasing salt concentrations (thus stabilizing the base pairing) and increasing temperature while remaining below the melting point (thus destabilizing the base pairing). Measurements have been made from 350 nm to 182 nm, and the spectral changes observed quantified using a Bayesian Markov chain Monte Carlo (MCMC) algorithm, which uses statistical methods to fit to experimental data. Based on literature H-D exchange experiments, we surmise that the cause of the spectral variations is the induction of transient single stranding of tracts in the DNA polymer, particularly those with significant content of the weaker AT base pairs. More detailed analysis of the LD data will require better nucleotide transition polarization assignments.

Quadratic X-Ray Magneto-Optical Effect upon Reflection in a Near-Normal-Incidence Configuration at theMEdges of3d-Transition Metals

We have observed a quadratic x-ray magneto-optical effect in near-normal-incidence reflection at the M edges of iron. The effect appears as the magnetically induced rotation of approximately 0.1 degrees of the polarization plane of linearly polarized x-ray radiation upon reflection. A comparison of the measured rotation spectrum with results from x-ray magnetic linear dichroism data demonstrates that this is the first observation of the Schäfer-Hubert effect in the x-ray regime. Ab initio density-functional theory calculations reveal that hybridization effects of the 3p core states necessarily need to be considered when interpreting experimental data. The discovered magneto-x-ray effect holds promise for future ultrafast and element-selective studies of ferromagnetic as well as antiferromagnetic materials.

Is DNA a worm-like chain in Couette flow? In search of persistence length, a critical review.

Persistence length is the foremost measure of DNA flexibility. Its origins lie in polymer theory which was adapted for DNA following the determination of BDNA structure in 1953. There is no single definition of persistence length used, and the links between published definitions are based on assumptions which may, or may not be, clearly stated. DNA flexibility is affected by local ionic strength, solvent environment, bound ligands and intrinsic sequence-dependent flexibility. This article is a review of persistence length providing a mathematical treatment of the relationships between four definitions of persistence length, including: correlation, Kuhn length, bending, and curvature. Persistence length has been measured using various microscopy, force extension and solution methods such as linear dichroism and transient electric birefringence. For each experimental method a model of DNA is required to interpret the data. The importance of understanding the underlying models, along with the assumptions required by each definition to determine a value of persistence length, is highlighted for linear dichroism data, where it transpires that no model is currently available for long DNA or medium to high shear rate experiments.

Folding and Membrane Insertion of the Pore-Forming Peptide Gramicidin Occur as a Concerted Process

Many antibiotic peptides function by binding and inserting into membranes. Understanding this process provides an insight into the fundamentals of both membrane protein folding and antibiotic peptide function. For the first time, in this work, flow-aligned linear dichroism (LD) is used to study the folding of the antibiotic peptide gramicidin. LD provides insight into the combined processes of peptide folding and insertion and has the advantage over other similar techniques of being insensitive to off-membrane aggregation events. By combining LD data with conventional measurements of protein fluorescence and circular dichroism, the mechanism of gramicidin insertion is elucidated. The mechanism consists of five separately assignable steps that include formation of a water-insoluble gramicidin aggregate, dissociation from the aggregate, partitioning of peptide to the membrane surface, oligomerisation on the surface and concerted insertion and folding of the peptide to the double-helical form of gramicidin. Measurement of the rates of each step shows that although changes in the fluorescence signal cease 10 s after the initiation of the process, the insertion of the peptide into the membrane is actually not complete for a further 60 min. This last membrane insertion phase is only apparent by measurement of LD and circular dichroism signal changes. In summary, this study demonstrates the importance of multi-technique approaches, including LD, in studies of membrane protein folding.

Circular and linear dichroism of proteins

Circular dichroism (CD) is an important technique in the structural characterisation of proteins, and especially for secondary structure determination. The CD of proteins can be calculated from first principles using the so-called matrix method, with an accuracy which is almost quantitative for helical proteins. Thus, for proteins of unknown structure, CD calculations and experimental data can be used in conjunction to aid structure analysis. Linear dichroism (LD) can be calculated using analogous methodology and has been used to establish the relative orientations of subunits in proteins and protein orientation in an environment such as a membrane. However, simple analysis of LD data is not possible, due to overlapping transitions. So coupling the calculations and experiment is an important strategy. In this paper, the use of LD for the determination of protein orientation and how these data can be interpreted with the aid of calculations, are discussed. We review methods for the calculation of CD spectra, focusing on semiempirical and ab initio parameter sets used in the matrix method. Lastly, a new web interface for online CD and LD calculation is presented.

A Polarized-Light Spectroscopy Study of Interactions of a Hairpin Polyamide with DNA

We here study the interactions of a polyamide with large DNA, and compare to those of minor groove binder distamycin (DST), including high ligand/DNA binding ratios. Specific as well as nonspecific binding is probed using polarized-light spectroscopy combined with singular value decomposition analysis. Circular and linear dichroism data confirm binding geometries consistent with minor groove binding for both of the ligands. Interestingly, at high and intermediate ligand/DNA ratios the polyamide exhibits no significant sequence discrimination between mixed-sequence (calf thymus) and AT DNA as compared to DST. Each ligand is concluded to exhibit two different binding modes depending upon ligand/DNA ratio and nucleo-base sequence. At high binding ratios, distinct differences between the ligands are observed: circular dichroism spectra exciton effects provide evidence of bimolecular interactions of the polyamide when bound to AT-DNA, whereas no effects are seen with DST or mixed-sequence DNA. Also linear dichroism indicates that a change in binding geometry occurs at high polyamide/AT ratios, and that the effect occurs only with polyamide in contrast to DST. Since the effect is insignificant with DST, or with calf thymus DNA, it is concluded that it relates to the sizes of the ligands and the minor grooves, becoming critical in the limit of crowding.

Dynamic mechanical analysis and dynamic infrared linear dichroism study of the frequency-dependent viscoelastic behavior of a poly(ester urethane)

Dynamic infrared linear dichroism (DIRLD) data have been collected as a function of strain modulation frequency in a simultaneous DIRLD-dynamic mechanical analysis experiment. The frequency range is limited, but the DIRLD data indicate some similarities to the temperature-dependent data. The frequency-dependent infrared data do not show the direct correlation with the mechanical data that was evident in the temperature-dependent study. However, the frequency-dependent infrared data do provide some molecular insight, with a similarity to the temperature-dependent results in the 1800–1320 cm −1 region, a quadrature signal increasing with increasing frequency in the 1320–1000 cm −1 region, and complex changes in the low wavenumber region that are interpreted as polymer chain responses as a function of frequency.

A DNA‐Binding Copper(I) Metallosupramolecular Cylinder that Acts as an Artificial Nuclease

The DNA binding of a dicationic pyridylimine-based dicopper(I) metallosupramolecular cylinder is reported together with its ability to act as an artificial nuclease. The cylinder binds strongly to DNA; more strongly than the spherical dication [Ru(phen)(3)](2+) (phen=1,10-phenanthroline), but more weakly than the corresponding tetracationic cylinders. DNA coiling effects are not observed with this dication, in contrast to the situation with the previously reported tetracationic cylinder involving a similar ligand. Linear dichroism (LD) data suggests that the dicopper cylinder binds in a different orientation from that of the tetracationic iron cylinder. Furthermore, the dicopper cylinder shows DNA-cleavage activity in the presence of peroxide. Of particular note is that the cylinder displays a marked and unusual ability to cleave both DNA strands at the same site, probably reflecting its dinuclear nature and possibly its mode of binding to the DNA.

Quantitation of protein orientation in flow-oriented unilamellar liposomes by linear dichroism

The linear dichroism of the visible wavelength transitions of retinal have been used to analyse linear dichroism spectra to determine the orientation of aromatic and peptide structural motifs of Bacteriorhodopsin incorporated into unilamellar soy bean liposomes. The results are consistent with the available X-ray data. This proves that visible light absorbing chromophores can be used to analyse linear dichroism data to give the orientation of membrane proteins in membrane mimicking environments. The work has been extended by screening a wide range of hydrophobic molecules with high extinction coefficients in transitions above 300 nm to find molecules that could be used as independent probes of liposome orientation for experiments involving proteins incorporated into liposomes. Three probes were found to have potential for future work: bis-(1,3-dibutylbarbituric acid)pentamethine oxonol (DiBAC 4), retinol and rhodamine B. All three can be used to determine the orientation of the porphyrin of cytochrome c, the aromatic residues of gramicidin and the helices of both proteins. The orientation parameter, S, for the liposomes varied from batch to batch of unilamellar liposomes prepared by extruding through a 100 nm membrane. The value and variation in S was 0.030 ± 0.010. Repeat experiments with the same batch of liposomes showed less variation. Film LD data were measured for DiBAC 4 and rhodamine B to determine the polarisations of their long wavelength transitions.

The vibrational structure of (E,E′)-1,4-diphenyl-1,3-butadiene: Linear dichroism FT-IR spectroscopy and quantum chemical calculations

The title compound (DPB) was investigated by FT-IR spectroscopy in liquid solutions and by FT-IR linear dichroism (LD) measurements on samples aligned in stretched polyethylene. The LD data provided experimental assignments of molecular transition moment directions and vibrational symmetries for more than 40 vibrational transitions. The observed IR wavenumbers, relative intensities, and polarization directions were generally well reproduced by the results of a harmonic analysis based on B3LYP/cc-pVTZ density functional theory (DFT). The combined experimental and theoretical results led to proposal of a nearly complete assignment of the IR active fundamentals of DPB, involving reassignment of a number of transitions. In addition, previously published Raman spectra of DPB were well predicted by the B3LYP/cc-pVTZ calculations.

Excitation energy migration in uniaxially oriented polymer films: A comparison between strongly and weakly organized systems

The mechanism of multistep excitation energy migration in uniaxially oriented polymer films is discussed for strongly and weakly orientating dyes in poly(vinyl alcohol) matrix. The comparison between both types of systems is based on concentration depolarization of fluorescence, Monte-Carlo simulations and linear dichroism data. It is found that the alignment of transition dipole moments of fluorophores in the ordered matrix relative to the direction of polymer stretching exhibits strong effect on the concentration depolarization of fluorescence. In ordered matrices of flavomononucleotide and rhodamine 6G concentration depolarization of fluorescence remains quite strong, whereas for linear carbocyanines it is very weak despite effective energy migration.

Intramolecular hydrogen bonding. Spectroscopic and theoretical studies of vibrational transitions in dibenzoylmethane enol

The vibrational structure of the title compound (DBM) was investigated by FTIR spectroscopy in liquid solutions, by FTIR linear dichroism (LD) measurements, and by Raman spectroscopy. The results were supported by the application of theoretical model calculations and analyzed with particular attention to the possible origin of the broad, very strong, and irregularly shaped absorbance band observed in the 1700–1400 cm −1 region. The orientation factors derived from the observed LD data indicate that rotational dynamics of the phenyl groups do not contribute significantly to the broadening of the band. The position of the two sharp Evans transmission windows near 1580 and 1500 cm −1 is unaffected by deuteration of the reactive protons in DBM. The transmissions coincide with prominent peaks in the Raman spectrum and can be assigned to combinations of phenylic modes (9a, 18a) with low IR intensity, but large Raman scattering activity.

A new method for fibrous protein analysis illustrated by application to tubulin microtubule polymerisation and depolymerisation

A thermostatted micro volume Couette cell has been designed to enable linear dichroism (LD) data to be collected at a range of temperatures. The cell is a development of the traditional Couette flow LD cell and includes the recent development of micro-volume LD (20-40 microL) coupled with the addition of a heating element, temperature probe and controller. This new micro volume Couette LD cell opens the way not only to the LD analysis of systems where sample volume is critical, but also for the LD analysis of temperature sensitive samples. The polymerization of the microtubule protein tubulin has been followed in a range of different conditions using the thermostatted micro volume Couette LD cell. The focusing lenses on the cell, which are required for the microvolume cell, have the side benefit of significantly reducing the light-scattering artifacts caused by the large size of tubulin microtubules. It is now possible to monitor real-time polymerization and depolymerization kinetics, and any structural rearrangements of chromophores within the polymer. In the case of tubulin, the LD spectra revealed a greater change in the orientation of tryptophan residues at approximately 290 nm during polymerization compared to other contributing chromophores-guanine, phenylalanine, and tyrosine. The improvements in instrumental design have also allowed LD spectra of tubulin to be collected down to approximately 230 nm (previous data have only been available from the near UV region), which means that some indication of protein backbone-orientation changes are now available. It was observed during this work that apparent LD intensity maxima are in fact artifacts when the high-tension voltage is high. The onset of such artifacts has been observed at much lower voltages with light-scattering fibrous proteins (including tubulin) than with nonscattering samples. Therefore, caution must be used when interpreting LD data collected with medium to high photomultiplier tube voltages.

Disorder Influence on Linear Dichroism Analyses of Smectic Phases

Linear dichroism, the unequal absorption of parallel and perpendicular linear polarized light, is often used to determine the anisotropic ordering of rodlike polymers in a smectic phase, such as helices in a lipid bilayer. It is a measure of two properties of the sample: 1), orientation of the chromophore transition dipole moment (TDM) and 2), disorder. Since it is the orientation of the chromophore TDM that is needed for high resolution structural studies, it is imperative to either deconvolve sample disorder, or at a minimum, estimate its effect upon the calculated TDM orientation. Herein, a rigorous analysis of the effects of disorder is undertaken based on the recently developed Gaussian disorder model implemented in linear dichroism data. The calculation of both the rod tilt and rotational pitch angles as a function of the disorder and dichroism, yield the following conclusions: Disorders smaller than 5° have a vanishingly small effect on the calculated polymer orientation, whereas values smaller than 10° have a negligible effect on the calculated parameters. Disorders larger than 10° have an appreciable effect on the calculated orientational parameters and as such must be estimated before any structural characterization. Finally the theory is tested on the HIV vpu transmembrane domain, employing experimental mosaicity measurements from x-ray reflectivity rocking scans and linear dichroism.